Looking for a tool for eukaryotic and diploid genome annotation

Question

[Rox]

Hi everyone !

I'm actually looking for a good tool in order to do de novo annotation of a diploid genome assembly of D. suzukii. My reference is also a diploid version of the D. melanogaster.

I've heard about Maker, but I never used it and I don't know if it's suitable for diploid genomes.

Any ideas ?

Thanks a lot !

Cheers,

Roxane

Answer 1

[Juke34]

It doesn't make any difference, from what I know. It should work perfectly fine.

More you will use ab-initio tool within maker, better the result should be. So, for Augustus you already have an hmm profile available. For the others(Snap, Genemark,...), I guess you have to train yourself the tool.

Other solution will be to use Augustus standalone. If you feed it with some evidence data it will give even better result. Or to use Breaker. But If you plan to use some protein data set, I will go for Maker. It should better than Breaker and it does the repeat annotation for you.

Best

[Rox]

Thanks for your answer !

Actually, it's my first time using a annotation tool, I'm a beginner so I first have to read a lot before to use correctly the tool.

Augustus is also a annotation tool ? What is an HMM profile exactly ?

[Juke34]

Annotation tool ~ prediction tool ~ Gene finding ... for me distinction between them has been blurred these last years. As Augustus allows to predict as well UTR in some species (In drosophila as example) I call it annotation tool. For purist it will be just a gene predictor. As you prefer. An HMM profile it's a Hidden Markov model, or more generally a probabilistic model. Here it determines gene models based on the statistical properties of protein-coding sequence (e.g codon usage, GC content, nucleotide periodicity, etc = gene content) and signal detection as ORF, splice site, start codon, etc.

You should read that it's a really good start: Mark Yandell & Daniel Ence Nature Reviews Genetics 13, 329-342 (May 2012) doi:10.1038/nrg3174